T Cells Summary (All)
Stanley
1/2/2018
All T cell data
Sample Summary for all T cells
# A tibble: 7 x 2
Group N
<fctr> <int>
1 Aged.Female.Brain.NoStim 5
2 Aged.Female.Brain.PlusStim 5
3 Aged.Male.Brain.NoStim 6
4 Aged.Male.Brain.PlusStim 4
5 Aged.Male.Spleen.NoStim 5
6 Aged.Male.Spleen.PlusStim 5
7 Young.Male.Brain.NoStim 5Normalize and Filter the data
before normalization
lib.size norm.factors
AgedFemale.Brain.NoStim.13_S10 9655634 1
AgedFemale.Brain.NoStim.14_S1 14866050 1
AgedFemale.Brain.NoStim.15_S6 6654543 1
AgedFemale.Brain.NoStim.16_S12 10970566 1
AgedFemale.Brain.NoStim.17_S8 12591901 1
AgedFemale.Brain.PlusStim.23_S11 4920738 1
AgedFemale.Brain.PlusStim.24_S9 6062158 1
AgedFemale.Brain.PlusStim.25_S5 9203922 1
AgedFemale.Brain.PlusStim.26_S1 3954801 1
AgedFemale.Brain.PlusStim.27_S8 2216762 1
AgedMale.Brain.NoStim.10_S9 19573103 1
AgedMale.Brain.NoStim.11_S10 18771250 1
AgedMale.Brain.NoStim.12_S11 20589456 1
AgedMale.Brain.NoStim.7_S6 24973886 1
AgedMale.Brain.NoStim.8_S7 10293283 1
AgedMale.Brain.NoStim.9_S8 16088402 1
AgedMale.Brain.PlusStim.19_S4 6391537 1
AgedMale.Brain.PlusStim.20_S3 2241662 1
AgedMale.Brain.PlusStim.21_S7 3850380 1
AgedMale.Brain.PlusStim.22_S2 1156594 1
AgedMaleSpleenNoStim30_S10 8998764 1
AgedMaleSpleenNoStim31_S7 9213356 1
AgedMaleSpleenNoStim32_S12 9650685 1
AgedMaleSpleenNoStim33_S3 14709415 1
AgedMaleSpleenNoStim34_S4 10176505 1
AgedMaleSpleenPlusStim36_S2 11101911 1
AgedMaleSpleenPlusStim37_S6 9932756 1
AgedMaleSpleenPlusStim38_S5 8586075 1
AgedMaleSpleenPlusStim39_S9 6745077 1
AgedMaleSpleenPlusStim40_S11 11188159 1
YoungMale.Brain.NoStim.2_S1 15470386 1
YoungMale.Brain.NoStim.3_S2 15558582 1
YoungMale.Brain.NoStim.4_S3 12213798 1
YoungMale.Brain.NoStim.5_S4 12781536 1
YoungMale.Brain.NoStim.6_S5 13326420 1before filtering low-count genes
dim.y.counts.
total number of genes detected 38924
total sample number 35keep the genes that have more than 1 count per million (cpm) in at least 2 samples
dim.y.counts.
total number of genes after filtering 12638
total sample number 35normalize the filtered genes across all samples
lib.size norm.factors
AgedFemale.Brain.NoStim.13_S10 8450652 1.346
AgedFemale.Brain.NoStim.14_S1 12829959 1.249
AgedFemale.Brain.NoStim.15_S6 5775658 1.110
AgedFemale.Brain.NoStim.16_S12 9689366 1.200
AgedFemale.Brain.NoStim.17_S8 10768556 1.200
AgedFemale.Brain.PlusStim.23_S11 3558217 0.780
AgedFemale.Brain.PlusStim.24_S9 3879926 0.589
AgedFemale.Brain.PlusStim.25_S5 6195711 0.559
AgedFemale.Brain.PlusStim.26_S1 2247330 0.941
AgedFemale.Brain.PlusStim.27_S8 1083591 0.692
AgedMale.Brain.NoStim.10_S9 16743058 0.998
AgedMale.Brain.NoStim.11_S10 16260522 1.018
AgedMale.Brain.NoStim.12_S11 17521858 0.967
AgedMale.Brain.NoStim.7_S6 21581567 0.966
AgedMale.Brain.NoStim.8_S7 9004501 0.792
AgedMale.Brain.NoStim.9_S8 13854192 0.925
AgedMale.Brain.PlusStim.19_S4 4919751 0.797
AgedMale.Brain.PlusStim.20_S3 1531051 1.010
AgedMale.Brain.PlusStim.21_S7 2536233 0.631
AgedMale.Brain.PlusStim.22_S2 746962 0.859
AgedMaleSpleenNoStim30_S10 7317320 1.511
AgedMaleSpleenNoStim31_S7 7520542 1.461
AgedMaleSpleenNoStim32_S12 7904050 1.439
AgedMaleSpleenNoStim33_S3 12378836 1.460
AgedMaleSpleenNoStim34_S4 8315177 1.433
AgedMaleSpleenPlusStim36_S2 8927352 1.108
AgedMaleSpleenPlusStim37_S6 7522045 1.149
AgedMaleSpleenPlusStim38_S5 6625479 1.189
AgedMaleSpleenPlusStim39_S9 5092337 1.252
AgedMaleSpleenPlusStim40_S11 8254639 1.057
YoungMale.Brain.NoStim.2_S1 13277300 0.864
YoungMale.Brain.NoStim.3_S2 13244514 0.679
YoungMale.Brain.NoStim.4_S3 10078524 0.959
YoungMale.Brain.NoStim.5_S4 10953635 1.009
YoungMale.Brain.NoStim.6_S5 11336934 0.969Overview on the data samples
MDS plot: to check the distance between each sample
MDS plot
